Parameter inference in differential equation models of biopathways using time warped gradient matching

Mu Niu*, Simon Rogers, Maurizio Filippone, Dirk Husmeier

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

Parameter inference in mechanistic models of biopathways based on systems of coupled differential equations is a topical yet computationally challenging problem due to the fact that each parameter adaptation involves a numerical integration of the differential equations. Techniques based on gradient matching, which aim to minimize the discrepancy between the slope of a data interpolant and the derivatives predicted from the differential equations, offer a computationally appealing shortcut to the inference problem. Gradient matching critically hinges on the smoothing scheme for function interpolation, with spurious oscillations in the interpolant having a dramatic effect on the subsequent inference. The present article demonstrates that a time warping approach that aims to homogenize intrinsic functional length scales can lead to a significant improvement in parameter estimation accuracy. We demonstrate the effectiveness of this scheme on noisy data from a dynamical system with periodic limit cycle, and a biopathway model.

Original languageEnglish (US)
Title of host publicationComputational Intelligence Methods for Bioinformatics and Biostatistics - 13th International Meeting, CIBB 2016, Revised Selected Papers
EditorsGiulio Caravagna, Roberto Tagliaferri, David Gilbert, Andrea Bracciali
PublisherSpringer Verlag
Pages145-159
Number of pages15
ISBN (Print)9783319678337
DOIs
StatePublished - 2017
Event13th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2016 - Stirling, United Kingdom
Duration: Sep 1 2016Sep 3 2016

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume10477 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference13th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2016
Country/TerritoryUnited Kingdom
CityStirling
Period09/1/1609/3/16

Bibliographical note

Publisher Copyright:
© Springer International Publishing AG 2017.

Keywords

  • Biopathways
  • Differential equations
  • Gradient matching
  • Optimisation
  • Reproducing kernel hilbert space
  • Time warping

ASJC Scopus subject areas

  • Theoretical Computer Science
  • General Computer Science

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